@schamane:
Personally, I'd appreciate it if the bug (adding wp-admin to relative links) was fixed.
Try adding this to that array in tiny_mce_config.php, see if it works:
'document_base_url' => get_option('url'),
If it does, I'll see about getting it into trac.
@skeezicks:
It may not help with their frustration, but it will help them prevent problems in the future by using correct absolute URLs instead of relative ones. When they start using non-default permalinks and suddenly every link they've ever made breaks, well, then we have to tell them "yeah, you messed up originally, go undo all that work you've done for the last long time period", then that's a tad more frustrating, no?
Relative URLs are tools of evil and should be avoided whenever possible.